From 2f0a0ebeed136b64dba2286abd72c1ff3e055d91 Mon Sep 17 00:00:00 2001
From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 30 Jul 2014 21:22:08 +0000
Subject: [PATCH] in progress

---
 forester/java/src/org/forester/archaeopteryx/MainFrame.java |   10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 28d0ae3..e89f978 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -548,10 +548,16 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {
             return;
         }
-        List<PhylogenyNode> nodes = null;
+        List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
-            nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
+            final List<PhylogenyNode>  all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
+            for( final PhylogenyNode n : all_selected_nodes ) {
+                if ( n.isExternal() ) {
+                    nodes.add( n );
+                }
+            }
         }
+        
         String function = "Retain";
         if ( delete ) {
             function = "Delete";
-- 
1.7.10.2